Porcine single nucleotide polymorphisms and their functional effect: an update

• Published in: BMC research notes Vol. 11; no. 1; p. 860
• Main Authors: Keel, B N, Nonneman, D J, Lindholm-Perry, A K, Oliver, W T, Rohrer, G A
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 04.12.2018; BioMed Central; BMC
• Subjects: Animals; Bioinformatics; Cattle; Deoxyribonucleic acid; DNA; DNA - classification; DNA - genetics; DNA - isolation & purification; Fertility; Functional variation; Gene Ontology; Genes; Genetic testing; Genome; Genome sequence; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genomics; Germplasm; High-Throughput Nucleotide Sequencing; Hogs; Loss-of-function; Male; Molecular Sequence Annotation; Nucleotide sequence; Ontology; Polymorphism, Single Nucleotide; Proteins; Research Note; Semen - chemistry; Single-nucleotide polymorphism; Studies; Swine; Tail - chemistry; Untranslated Regions; United States > US; Loss-of-function; Functional variation; Genome sequence; Swine
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-018-3973-6

To aid in the development of a comprehensive list of functional variants in the swine genome, single nucleotide polymorphisms (SNP) were identified from whole genome sequence of 240 pigs. Interim data from 72 animals in this study was published in 2017. This communication extends our previous work not only by utilizing genomic sequence from additional animals, but also by the use of the newly released Sscrofa 11.1 reference genome. A total of 26,850,263 high confidence SNP were identified, including 19,015,267 reported in our previously published results. Variation was detected in the coding sequence or untranslated regions (UTR) of 78% of the genes in the porcine genome: 1729 loss-of-function variants were predicted in 1162 genes, 12,686 genes contained 64,232 nonsynonymous variants, 250,403 variants were present in UTR of 15,739 genes, and 15,284 genes contained 90,939 synonymous variants. In total, approximately 316,000 SNP were classified as being of high to moderate impact (i.e. loss-of-function, nonsynonymous, or regulatory). These high to moderate impact SNP will be the focus of future genome-wide association studies.